BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068150.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 3,588,119 number of mapped reads = 3,376,922 (94.11%) number of supplementary alignments = 23,839 (0.66%) number of secondary alignments = 0 number of mapped bases = 212,941,743 bp number of sequenced bases = 212,845,514 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,145,830 duplication rate = 20.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6072 >>>>>>> ACTG content number of A's = 54,610,781 bp (25.66%) number of C's = 36,972,684 bp (17.37%) number of T's = 70,994,312 bp (33.35%) number of G's = 50,245,249 bp (23.61%) number of N's = 22,488 bp (0.01%) GC percentage = 40.98% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,190,353 number of insertions = 13,069 mapped reads with insertion percentage = 0.38% number of deletions = 54,228 mapped reads with deletion percentage = 1.59% homopolymer indels = 47.17% >>>>>>> Coverage mean coverageData = 0.0688X std coverageData = 1.3876X There is a 2.34% of reference with a coverageData >= 1X There is a 1.38% of reference with a coverageData >= 2X There is a 0.95% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.3% of reference with a coverageData >= 6X There is a 0.21% of reference with a coverageData >= 7X There is a 0.14% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 37592537 0.15082224007778902 0.9585580939895976 chr2 243199373 18133339 0.07456161903838461 1.114472361487916 chr3 198022430 14513560 0.07329250529851593 0.6219292683008153 chr4 191154276 7984213 0.04176842478794458 0.47727663555974487 chr5 180915260 17828886 0.09854827061022935 0.7175515082875713 chr6 171115067 9714470 0.056771564131170286 0.6143761832074038 chr7 159138663 24310010 0.15275992358940454 5.381585884906854 chr8 146364022 6870094 0.04693840676228479 0.6909396416451189 chr9 141213431 10336834 0.07320007683971647 0.6459092764669596 chr10 135534747 5227418 0.038568840210400065 0.4895833248458614 chr11 135006516 8855469 0.06559290071599211 0.6235426070604866 chr12 133851895 9781029 0.07307351905626738 0.633547137533074 chr13 115169878 4341029 0.03769239904899439 0.4669385511259371 chr14 107349540 4572324 0.04259286066805689 0.4839106778557347 chr15 102531392 3961701 0.038638907779580324 0.47449660509181485 chr16 90354753 5225517 0.05783333833030344 0.5417483455812107 chr17 81195210 3682594 0.04535481834457969 0.5024199709871826 chr18 78077248 4669745 0.05980929297098177 0.9025093027438548 chr19 59128983 2538305 0.04292827089550991 0.5524506869875107 chr20 63025520 2422522 0.03843716005833827 0.44837639599017703 chr21 48129895 1966829 0.04086501746991137 0.46400418575247576 chr22 51304566 1531244 0.029846154433895804 0.3862942359138951 chrMT 16571 189324 11.425019612576188 9.710701997950832 chrX 155270560 5659364 0.03644840335476345 0.43584871025813327 chrY 59373566 1033386 0.017404816143264834 0.2837803999280523